For the Arceus event, Mystery Gift must be used to receive a Wonder Card with the Azure Flute, which should then be retrieved from the Poké Mart deliveryman (as modifying the save file to directly add the Azure Flute to the Bag will not affect the flag responsible for activating the event). The player must also enter the Hall of Fame and obtain the National Pokédex to be able to use the Azure Flute. When the player reaches the Spear Pillar at the top of Mt. Coronet and steps one tile north from the entrance, he or she will be prompted to use the flute, which will play a unique and eerie tune and reload the Spear Pillar map with a steep staircase that leads to the Hall of Origin. After it is used and once Arceus is caught, the Azure Flute will no longer trigger the entrance to the Hall of Origin when played at the Spear Pillar and the message "The Azure Flute echoed hollowly..." will appear. Should the player knock out Arceus, then the Azure Flute can be used to summon Arceus again.

Junichi Masuda revealed in an interview with Nintendo World Report in 2013 that the Azure Flute was thought to be too confusing for players to use, leading to the decision to not distribute it.[1]

Despite the Azure Flute never having been distributed, the Wonder Card text for the Arceus set to be distributed for Pokémon's 20th Anniversary makes reference to it.